def configure(self, profile, statsResults):
self.configDlg = ConfigureDialog(Ui_MultCompCorrectionDialog)
self.connect(self.configDlg.ui.btnXmaxFig1, QtCore.SIGNAL('clicked()'),
self.setXaxisMax1)
self.connect(self.configDlg.ui.btnXmaxFig2, QtCore.SIGNAL('clicked()'),
self.setXaxisMax2)
self.connect(self.configDlg.ui.btnXmaxFig3, QtCore.SIGNAL('clicked()'),
self.setXaxisMax3)
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigHeight.setValue(self.figHeight)
self.configDlg.ui.spinBinWidth.setValue(self.binWidth)
self.configDlg.ui.chkLogScale.setChecked(self.yAxisLogScale)
self.configDlg.ui.spinXlimitFig1.setValue(self.xLimitFig1)
self.configDlg.ui.spinXlimitFig2.setValue(self.xLimitFig2)
self.configDlg.ui.spinXlimitFig3.setValue(self.xLimitFig3)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeight = self.configDlg.ui.spinFigHeight.value()
self.binWidth = self.configDlg.ui.spinBinWidth.value()
self.yAxisLogScale = self.configDlg.ui.chkLogScale.isChecked()
self.xLimitFig1 = self.configDlg.ui.spinXlimitFig1.value()
self.xLimitFig2 = self.configDlg.ui.spinXlimitFig2.value()
self.xLimitFig3 = self.configDlg.ui.spinXlimitFig3.value()
self.settings.setValue(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/height', self.figHeight)
self.settings.setValue(self.name + '/histogram log scale',
self.yAxisLogScale)
self.settings.setValue(self.name + '/bin width', self.binWidth)
self.settings.setValue(self.name + '/histogram x-axis limit',
self.xLimitFig1)
self.settings.setValue(self.name + '/correction plot x-axis limit',
self.xLimitFig2)
self.settings.setValue(
self.name + '/significant features x-axis limit',
self.xLimitFig3)
self.plot(profile, statsResults)
def configure(self, profile, statsResults):
configDlg = ConfigureDialog(Ui_ScatterPlotDialog)
configDlg.ui.spinNumBins.setEnabled(self.bShowHistograms)
configDlg.ui.spinHistogramSize.setEnabled(self.bShowHistograms)
configDlg.ui.spinFigWidth.setValue(self.figWidth)
configDlg.ui.spinFigHeight.setValue(self.figHeight)
configDlg.ui.chkShowCIs.setChecked(self.bShowCIs)
configDlg.ui.spinNumBins.setValue(self.numBins)
configDlg.ui.spinHistogramSize.setValue(self.histogramSize)
configDlg.ui.chkShowHistogram.setChecked(self.bShowHistograms)
configDlg.ui.spinMarkerSize.setValue(self.markerSize)
configDlg.ui.chkShowR2.setChecked(self.bShowR2)
if configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = configDlg.ui.spinFigWidth.value()
self.figHeight = configDlg.ui.spinFigHeight.value()
self.bShowCIs = configDlg.ui.chkShowCIs.isChecked()
self.numBins = configDlg.ui.spinNumBins.value()
self.histogramSize = configDlg.ui.spinHistogramSize.value()
self.bShowHistograms = configDlg.ui.chkShowHistogram.isChecked()
self.markerSize = configDlg.ui.spinMarkerSize.value()
self.bShowR2 = configDlg.ui.chkShowR2.isChecked()
self.settings.setValue(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/height', self.figHeight)
self.settings.setValue(self.name + '/show CIs', self.bShowCIs)
self.settings.setValue(self.name + '/bin', self.numBins)
self.settings.setValue(self.name + '/bin size', self.histogramSize)
self.settings.setValue(self.name + '/show histograms',
self.bShowHistograms)
self.settings.setValue(self.name + '/marker size', self.markerSize)
self.settings.setValue(self.name + '/show R2', self.bShowR2)
self.plot(profile, statsResults)
def configure(self, profile, statsResults):
self.statsResults = statsResults
self.configDlg = ConfigureDialog(Ui_ExtendedErrorBarDialog)
# set enabled state of controls
self.configDlg.ui.cboPercentageOrSeqCount.setEnabled(self.bShowBarPlot)
self.configDlg.ui.spinMinimumX.setEnabled(self.bCustomLimits)
self.configDlg.ui.spinMaximumX.setEnabled(self.bCustomLimits)
# set current value of controls
self.configDlg.ui.cboSortingField.setCurrentIndex(
self.configDlg.ui.cboSortingField.findText(self.sortingField))
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigRowHeight.setValue(self.figHeightPerRow)
self.configDlg.ui.chkShowBarPlot.setChecked(self.bShowBarPlot)
self.configDlg.ui.chkPValueLabels.setChecked(self.bShowPValueLabels)
self.configDlg.ui.chkCorrectedPvalues.setChecked(
self.bShowCorrectedPvalues)
self.configDlg.ui.chkCustomLimits.setChecked(self.bCustomLimits)
self.configDlg.ui.spinMinimumX.setValue(self.minX)
self.configDlg.ui.spinMaximumX.setValue(self.maxX)
self.configDlg.ui.spinMarkerSize.setValue(self.markerSize)
self.configDlg.ui.cboPercentageOrSeqCount.setCurrentIndex(
self.configDlg.ui.cboPercentageOrSeqCount.findText(
self.percentageOrSeqCount))
if self.legendPos == 2:
self.configDlg.ui.radioLegendPosUpperLeft.setChecked(True)
elif self.legendPos == 3:
self.configDlg.ui.radioLegendPosLowerLeft.setChecked(True)
elif self.legendPos == 4:
self.configDlg.ui.radioLegendPosLowerRight.setChecked(True)
elif self.legendPos == 8:
self.configDlg.ui.radioLegendPosLowerCentre.setChecked(True)
else:
self.configDlg.ui.radioLegendPosNone.setChecked(True)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
QtGui.QApplication.instance().setOverrideCursor(
QtGui.QCursor(QtCore.Qt.WaitCursor))
self.sortingField = str(
self.configDlg.ui.cboSortingField.currentText())
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeightPerRow = self.configDlg.ui.spinFigRowHeight.value()
self.bShowBarPlot = self.configDlg.ui.chkShowBarPlot.isChecked()
self.bShowPValueLabels = self.configDlg.ui.chkPValueLabels.isChecked(
)
self.bShowCorrectedPvalues = self.configDlg.ui.chkCorrectedPvalues.isChecked(
)
self.bCustomLimits = self.configDlg.ui.chkCustomLimits.isChecked()
self.minX = self.configDlg.ui.spinMinimumX.value()
self.maxX = self.configDlg.ui.spinMaximumX.value()
self.markerSize = self.configDlg.ui.spinMarkerSize.value()
self.percentageOrSeqCount = self.configDlg.ui.cboPercentageOrSeqCount.currentText(
)
# legend position
if self.configDlg.ui.radioLegendPosUpperLeft.isChecked() == True:
self.legendPos = 2
elif self.configDlg.ui.radioLegendPosLowerLeft.isChecked() == True:
self.legendPos = 3
elif self.configDlg.ui.radioLegendPosLowerCentre.isChecked(
) == True:
self.legendPos = 8
elif self.configDlg.ui.radioLegendPosLowerRight.isChecked(
) == True:
self.legendPos = 4
else:
self.legendPos = -1
self.settings.setValue(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/row height',
self.figHeightPerRow)
self.settings.setValue(self.name + '/field', self.sortingField)
self.settings.setValue(self.name + '/sequences subplot',
self.bShowBarPlot)
self.settings.setValue(self.name + '/p-value labels',
self.bShowPValueLabels)
self.settings.setValue(self.name + '/show corrected p-values',
self.bShowCorrectedPvalues)
self.settings.setValue(self.name + 'use custom limits',
self.bCustomLimits)
self.settings.setValue(self.name + '/minimum', self.minX)
self.settings.setValue(self.name + '/maximum', self.maxX)
self.settings.setValue(self.name + '/marker size', self.markerSize)
self.settings.setValue(self.name + '/percentage or seq count',
self.percentageOrSeqCount)
self.settings.setValue(self.name + '/legend position',
self.legendPos)
self.plot(profile, statsResults)
QtGui.QApplication.instance().restoreOverrideCursor()
def configure(self, profile, statsResults):
configDlg = ConfigureDialog(Ui_ProfileBarPlotDialog)
# set enabled state of widgets
configDlg.ui.spinEndCapSize.setEnabled(self.bShowCIs)
configDlg.ui.spinPvalueThreshold.setEnabled(self.bShowPvalue)
# set current values
configDlg.ui.cboFieldToPlot.setCurrentIndex(
configDlg.ui.cboFieldToPlot.findText(self.fieldToPlot))
configDlg.ui.spinFigColWidth.setValue(self.figColWidth)
configDlg.ui.spinFigHeight.setValue(self.figHeight)
configDlg.ui.chkShowCIs.setChecked(self.bShowCIs)
configDlg.ui.spinEndCapSize.setValue(self.endCapSize)
configDlg.ui.spinFeaturesToShow.setValue(self.numFeaturesToShow)
# legend position
if self.legendPos == 0:
configDlg.ui.radioLegendPosBest.setDown(True)
elif self.legendPos == 1:
configDlg.ui.radioLegendPosUpperRight.setChecked(True)
elif self.legendPos == 7:
configDlg.ui.radioLegendPosCentreRight.setChecked(True)
elif self.legendPos == 4:
configDlg.ui.radioLegendPosLowerRight.setChecked(True)
elif self.legendPos == 2:
configDlg.ui.radioLegendPosUpperLeft.setChecked(True)
elif self.legendPos == 6:
configDlg.ui.radioLegendPosCentreLeft.setChecked(True)
elif self.legendPos == 3:
configDlg.ui.radioLegendPosLowerLeft.setChecked(True)
else:
configDlg.ui.radioLegendPosNone.setChecked(True)
configDlg.ui.spinBarWidth.setValue(self.barWidth)
configDlg.ui.chkShowPvalue.setChecked(self.bShowPvalue)
configDlg.ui.spinPvalueThreshold.setValue(self.pValueThreshold)
if configDlg.exec_() == QtGui.QDialog.Accepted:
self.fieldToPlot = str(configDlg.ui.cboFieldToPlot.currentText())
self.figColWidth = configDlg.ui.spinFigColWidth.value()
self.figHeight = configDlg.ui.spinFigHeight.value()
self.bShowCIs = configDlg.ui.chkShowCIs.isChecked()
self.endCapSize = configDlg.ui.spinEndCapSize.value()
self.numFeaturesToShow = configDlg.ui.spinFeaturesToShow.value()
# legend position
if configDlg.ui.radioLegendPosBest.isChecked() == True:
self.legendPos = 0
elif configDlg.ui.radioLegendPosUpperRight.isChecked() == True:
self.legendPos = 1
elif configDlg.ui.radioLegendPosCentreRight.isChecked() == True:
self.legendPos = 7
elif configDlg.ui.radioLegendPosLowerRight.isChecked() == True:
self.legendPos = 4
elif configDlg.ui.radioLegendPosUpperLeft.isChecked() == True:
self.legendPos = 2
elif configDlg.ui.radioLegendPosCentreLeft.isChecked() == True:
self.legendPos = 6
elif configDlg.ui.radioLegendPosLowerLeft.isChecked() == True:
self.legendPos = 3
else:
self.legendPos = -1
self.barWidth = configDlg.ui.spinBarWidth.value()
self.bShowPvalue = configDlg.ui.chkShowPvalue.isChecked()
self.pValueThreshold = configDlg.ui.spinPvalueThreshold.value()
self.settings.setValue(self.name + '/column width',
self.figColWidth)
self.settings.setValue(self.name + '/height', self.figHeight)
self.settings.setValue(self.name + '/field to plot',
self.fieldToPlot)
self.settings.setValue(self.name + '/legend position',
self.legendPos)
self.settings.setValue(self.name + '/show cis', self.bShowCIs)
self.settings.setValue(self.name + '/end cap size',
self.endCapSize)
self.settings.setValue(self.name + '/features to show',
self.numFeaturesToShow)
self.settings.setValue(self.name + '/bar width (%)', self.barWidth)
self.settings.setValue(self.name + '/show p-value',
self.bShowPvalue)
self.settings.setValue(self.name + '/p-value threshold',
self.pValueThreshold)
self.plot(profile, statsResults)
def configure(self, profile, statsResults):
self.statsResults = statsResults
configDlg = ConfigureDialog(Ui_BarConfigDialog)
configDlg.ui.cboFieldToPlot.clear()
configDlg.ui.cboFieldToPlot.addItem('Effect size')
configDlg.ui.cboFieldToPlot.addItem('Number of sequences')
configDlg.ui.cboFieldToPlot.addItem('Number of parental sequences')
configDlg.ui.cboFieldToPlot.addItem('p-values')
configDlg.ui.cboFieldToPlot.addItem('p-values (corrected)')
configDlg.ui.cboFieldToPlot.addItem('Proportion of sequences (%)')
configDlg.ui.cboFieldToPlot.setCurrentIndex(
configDlg.ui.cboFieldToPlot.findText(self.fieldToPlot))
configDlg.ui.chkSort.setChecked(self.bSortFeatures)
configDlg.ui.spinFigWidth.setValue(self.figWidth)
configDlg.ui.spinFigRowHeight.setValue(self.figHeightPerRow)
# legend position
if self.legendPos == 0:
configDlg.ui.radioLegendPosBest.setChecked(True)
elif self.legendPos == 1:
configDlg.ui.radioLegendPosUpperRight.setChecked(True)
elif self.legendPos == 7:
configDlg.ui.radioLegendPosCentreRight.setChecked(True)
elif self.legendPos == 4:
configDlg.ui.radioLegendPosLowerRight.setChecked(True)
elif self.legendPos == 2:
configDlg.ui.radioLegendPosUpperLeft.setChecked(True)
elif self.legendPos == 6:
configDlg.ui.radioLegendPosCentreLeft.setChecked(True)
elif self.legendPos == 3:
configDlg.ui.radioLegendPosLowerLeft.setChecked(True)
else:
configDlg.ui.radioLegendPosNone.setChecked(True)
if configDlg.exec_() == QtGui.QDialog.Accepted:
self.fieldToPlot = str(configDlg.ui.cboFieldToPlot.currentText())
self.bSortFeatures = configDlg.ui.chkSort.isChecked()
self.figWidth = configDlg.ui.spinFigWidth.value()
self.figHeightPerRow = configDlg.ui.spinFigRowHeight.value()
# legend position
self.bShowLegend = True
if configDlg.ui.radioLegendPosBest.isChecked() == True:
self.legendPos = 0
elif configDlg.ui.radioLegendPosUpperRight.isChecked() == True:
self.legendPos = 1
elif configDlg.ui.radioLegendPosCentreRight.isChecked() == True:
self.legendPos = 7
elif configDlg.ui.radioLegendPosLowerRight.isChecked() == True:
self.legendPos = 4
elif configDlg.ui.radioLegendPosUpperLeft.isChecked() == True:
self.legendPos = 2
elif configDlg.ui.radioLegendPosCentreLeft.isChecked() == True:
self.legendPos = 6
elif configDlg.ui.radioLegendPosLowerLeft.isChecked() == True:
self.legendPos = 3
else:
self.legendPos = -1
self.settings.setValue(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/row height',
self.figHeightPerRow)
self.settings.setValue(self.name + '/field to plot',
self.fieldToPlot)
self.settings.setValue(self.name + '/legend position',
self.legendPos)
self.settings.setValue(self.name + '/sort values',
self.bSortFeatures)
self.plot(profile, statsResults)
def configure(self, profile, statsResults):
self.profile = profile
self.configDlg = ConfigureDialog(Ui_SeqHistogramDialog)
self.connect(self.configDlg.ui.chkCustomBinWidth,
QtCore.SIGNAL('toggled(bool)'), self.changeCustomBinWidth)
self.connect(self.configDlg.ui.chkCustomXaxis,
QtCore.SIGNAL('toggled(bool)'), self.changeCustomXaxis)
self.connect(self.configDlg.ui.btnXmin, QtCore.SIGNAL('clicked()'),
self.setXaxisMin)
self.connect(self.configDlg.ui.btnXmax, QtCore.SIGNAL('clicked()'),
self.setXaxisMax)
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigHeight.setValue(self.figHeight)
self.configDlg.ui.chkCustomBinWidth.setChecked(self.bCustomBinWidth)
self.configDlg.ui.spinBinWidth.setValue(self.binWidth)
self.configDlg.ui.chkLogScale.setChecked(self.yAxisLogScale)
self.configDlg.ui.chkCustomXaxis.setChecked(self.bCustomXaxis)
self.configDlg.ui.spinXmin.setValue(self.xLimitLeft)
self.configDlg.ui.spinXmax.setValue(self.xLimitRight)
self.changeCustomBinWidth()
self.changeCustomXaxis()
# legend position
if self.legendPos == 0:
self.configDlg.ui.radioLegendPosBest.setDown(True)
elif self.legendPos == 1:
self.configDlg.ui.radioLegendPosUpperRight.setChecked(True)
elif self.legendPos == 7:
self.configDlg.ui.radioLegendPosCentreRight.setChecked(True)
elif self.legendPos == 4:
self.configDlg.ui.radioLegendPosLowerRight.setChecked(True)
elif self.legendPos == 2:
self.configDlg.ui.radioLegendPosUpperLeft.setChecked(True)
elif self.legendPos == 6:
self.configDlg.ui.radioLegendPosCentreLeft.setChecked(True)
elif self.legendPos == 3:
self.configDlg.ui.radioLegendPosLowerLeft.setChecked(True)
else:
self.configDlg.ui.radioLegendPosNone.setChecked(True)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeight = self.configDlg.ui.spinFigHeight.value()
self.bCustomBinWidth = self.configDlg.ui.chkCustomBinWidth.isChecked(
)
self.binWidth = self.configDlg.ui.spinBinWidth.value()
self.yAxisLogScale = self.configDlg.ui.chkLogScale.isChecked()
self.bCustomXaxis = self.configDlg.ui.chkCustomXaxis.isChecked()
self.xLimitLeft = self.configDlg.ui.spinXmin.value()
self.xLimitRight = self.configDlg.ui.spinXmax.value()
# legend position
if self.configDlg.ui.radioLegendPosBest.isChecked() == True:
self.legendPos = 0
elif self.configDlg.ui.radioLegendPosUpperRight.isChecked(
) == True:
self.legendPos = 1
elif self.configDlg.ui.radioLegendPosCentreRight.isChecked(
) == True:
self.legendPos = 7
elif self.configDlg.ui.radioLegendPosLowerRight.isChecked(
) == True:
self.legendPos = 4
elif self.configDlg.ui.radioLegendPosUpperLeft.isChecked() == True:
self.legendPos = 2
elif self.configDlg.ui.radioLegendPosCentreLeft.isChecked(
) == True:
self.legendPos = 6
elif self.configDlg.ui.radioLegendPosLowerLeft.isChecked() == True:
self.legendPos = 3
else:
self.legendPos = -1
self.settings.setValue(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/height', self.figHeight)
self.settings.setValue(self.name + '/custom bin width',
self.bCustomBinWidth)
self.settings.setValue(self.name + '/bin width', self.binWidth)
self.settings.setValue(self.name + '/log scale',
self.yAxisLogScale)
self.settings.setValue(self.name + '/custom x-axis extents',
self.bCustomXaxis)
self.settings.setValue(self.name + '/min value', self.xLimitLeft)
self.settings.setValue(self.name + '/max value', self.xLimitRight)
self.settings.setValue(self.name + '/legend position',
self.legendPos)
self.plot(profile, statsResults)
def configure(self, profile, statsResults):
self.statsResults = statsResults
self.configDlg = ConfigureDialog(Ui_pValueHistogramDialog)
self.connect(self.configDlg.ui.btnXmax, QtCore.SIGNAL('clicked()'),
self.setXaxisMax)
self.configDlg.ui.cboFieldToPlot.setCurrentIndex(
self.configDlg.ui.cboFieldToPlot.findText(self.fieldToPlot))
self.configDlg.ui.spinFigWidth.setValue(self.figWidth)
self.configDlg.ui.spinFigHeight.setValue(self.figHeight)
self.configDlg.ui.spinBinWidth.setValue(self.binWidth)
self.configDlg.ui.chkLogScale.setChecked(self.yAxisLogScale)
self.configDlg.ui.chkShowInset.setChecked(self.bShowInset)
self.configDlg.ui.spinInsetWidth.setValue(self.insetWidth)
self.configDlg.ui.spinInsetHeight.setValue(self.insetHeight)
self.configDlg.ui.spinInsetBinWidth.setValue(self.insetBinWidth)
self.configDlg.ui.spinXlimit.setValue(self.xLimit)
self.configDlg.ui.chkInsetLogScale.setChecked(self.insetLogScale)
if self.configDlg.exec_() == QtGui.QDialog.Accepted:
self.figWidth = self.configDlg.ui.spinFigWidth.value()
self.figHeight = self.configDlg.ui.spinFigHeight.value()
self.binWidth = self.configDlg.ui.spinBinWidth.value()
self.yAxisLogScale = self.configDlg.ui.chkLogScale.isChecked()
self.fieldToPlot = self.configDlg.ui.cboFieldToPlot.currentText()
self.bShowInset = self.configDlg.ui.chkShowInset.isChecked()
self.insetWidth = self.configDlg.ui.spinInsetWidth.value()
self.insetHeight = self.configDlg.ui.spinInsetHeight.value()
self.insetBinWidth = self.configDlg.ui.spinInsetBinWidth.value()
self.xLimit = self.configDlg.ui.spinXlimit.value()
self.insetLogScale = self.configDlg.ui.chkInsetLogScale.isChecked()
self.settings.setValue(self.name + '/width', self.figWidth)
self.settings.setValue(self.name + '/height', self.figHeight)
self.settings.setValue(self.name + '/field to plot',
self.fieldToPlot)
self.settings.setValue(self.name + '/histogram log scale',
self.yAxisLogScale)
self.settings.setValue(self.name + '/histogram bin width',
self.binWidth)
self.settings.setValue(self.name + '/show inset', self.bShowInset)
self.settings.setValue(self.name + '/inset width %',
self.insetWidth)
self.settings.setValue(self.name + '/inset height %',
self.insetHeight)
self.settings.setValue(self.name + '/inset log scale',
self.insetLogScale)
self.settings.setValue(self.name + '/inset bin width',
self.insetBinWidth)
self.settings.setValue(self.name + '/inset x-axis limit',
self.xLimit)
self.plot(profile, statsResults)
